IR Expansion Research Articles

Comparative Genomics and Phylogenetic Analyses of Aquarius macrophyllus and Related Genera in Alismataceae Based on Plastome Data.

Aquarius macrophyllus, an aquatic species native to South America, has been widely utilized as an ornamental plant. Although the plastome data have been commonly used in plant evolution and phylogenetics, research on the plastome of A. macrophyllus remains scarce. In this study, we sequenced the plastome of A. macrophyllus and conducted a comparative analysis incorporating eight species from related genera of Caldesia, Sagittaria, Alisma, and Luronium. The assembled plastome was 180,860 bp in size, with 133 genes annotated, including 88 protein-coding genes, 8 rRNA, and 37 tRNA. Comparative analyses showed that the genome lengths of the nine plastomes ranged from 159,063 to 180,860 bp, including a large single copy (LSC, 89,203-99,125 bp), a small single copy (SSC, 10,131-19,753 bp), and a pair of inverted repeat sequences (IR, 25,124-39,664 bp). The nine plastomes were similar in GC content, codon usage, and gene distribution but contained variations, including IR expansion in A. macrophyllus, loss of trnV-UAC introns, and gene inversion in Caldesia and Sagittaria species. Two sequence inversions of 5.6 and 6.4 kb were detected in Sagittaria and Caldesia, respectively. A total of 532 simple sequence repeats (SSRs) and 667 dispersed repeats were detected in the nine plastomes. Selection pressure analysis using A. macrophyllus as a reference to compare with other species revealed that three ribosomal protein genes rps2, rps18, and rps7 were positively selected, which showed intergeneric specificity, especially displaying higher selection pressure in Sagittaria species than that in Caldesia species. Phylogenetic analysis of Alismataceae elucidated that Alisma, Luronium, and Burnatia species were early diverged, followed by Hydrocleys and Limnocharis. The monophyly of Aquarius and its sister relationship with Echinodorus were revealed, supporting the classification of the new genus Aquarius. Our study enriches the genomic resources of Aquarius and provides new insights into plastome structure and evolution in Alismataceae.

Historical biogeography and plastome evolution of Commelinaceae Mirb. (Commelinales) corroborate the East Gondwanan origins

BackgroundCommelinaceae are a Pantropical monocot family comprising ca. 36 genera and 810 species. Due to the high morphological variation and limited sampling, the relationships within the family remain unclear. Previous studies, which relied on limited genetic loci or low-resolution sequencing, have not fully resolved these relationships. Additionally, there is a need to investigate the historical biogeography of Commelinaceae using genomic data. To address these issues, we assembled twelve Commelinaceae plastomes and inferred their biogeographical pathways using both newly generated and previously published data.ResultsOur results indicate that all members of the subfamily Commelinoideae have shortened accD and rpoA genes, which do not affect functionality. In contrast, members of the subf. Cartonematoideae possess intact forms of both genes. Phylogenetic analyses based on 79 plastid protein-coding genes provide much-needed insight into the placement of some key genera that had previously remained unplaced or were erroneously placed elsewhere within the family. Of these, our results support the monophyly of the subtribe Streptoliriinae, the non-monophyly of the subtr. Coleotrypinae, and the need to recognise a broader circumscription of Aneilema R.Br. (including Rhopalephora Hassk.). Our biogeographic analysis shows that the ancestor of Commelinaceae originated in the Australian region around 104.8 million years ago (Mya), thus revealing an East Gondwanan origin. We also found that four major dispersal events have shaped the intercontinental diversification of this family: (1) from the Australian to the Ethiopian region ca. 81.4 Mya; (2) from the Ethiopian to the Oriental + Palearctic region ca. 50.4 Mya; (3) from the Oriental + Palearctic to the Neotropical region ca. 50.4 Mya; and (4) from the Neotropical to the Ethiopian region ca. 32.3 Mya.ConclusionsWe identified genetic events, such as inversions and IR expansion, which shed light on the genomic evolution of Commelinaceae. Our findings support taxonomic updates, and future work will integrate comprehensive phylogenomic and morphological datasets to deepen our understanding of morphological evolution and biogeographic history within Commelinaceae, establishing a robust foundation for systematic revisions in the family.

Phylogenetic analysis of nine Impatiens species from subgenus Clavicarpa and subgenus Impatiens (Sect. Impatiens and Sect. Racemosae) based on chloroplast genomes.

The genus Impatiens L. ( Balsaminaceae) is one of the three most important bedding plant genera globally, valued for its medicinal, ornamental, and economic properties. However, the morphological overlap among species and the lack of genomic data have limited our understanding of their molecular phylogenetic relationships. This study involved the sequencing of the chloroplast genomes of 9 Impatiens species, including Impatiens lateristachys, Impatiens siculifer var. porphyrea, Impatiens apalophylla, Impatiens pritzelii, Impatiens menghuochengensis, Impatiens membranifolia, Impatiens qingchengshanica, Impatiens aquatilis, and Impatiens racemosa. The study evaluated sequence divergence by comparing genomic features, repeat sequences, codon usage, IR expansion and contraction, sequence alignment, and selective pressures. It then constructed phylogenetic relationships using the maximum likelihood method, revealing the evolutionary relationships among these species. The results indicated that the chloroplast genome sizes ranged from 151, 784 bp (I. racemosa) to 152, 628 bp (I. apalophylla), encoding between 108-115genes[77 to 81 protein-coding genes, 27 to 30 tRNA genes, and 4 rRNA genes]. Additionally, A detailed analysis was performed on the characteristics of repeat sequences, codon preferences, and IR region. Coding sections were more conserved than non-coding regions, and the IR regions were more conserved than the LSC and SSC regions, according to sequence variation and mutation hotspot analyses. The 9 species of Impatiens were classified into subgenus Clavicarpa and subgenus Impatiens, including the sections Impatiens and Racemosae, according to the phylogenetic tree. This study presents the chloroplast genomes of 9 species within the genus Impatiens, marking a novel attempt at using phylogenetic analysis to determine the taxonomic positions of Impatiens species. It provides new molecular evidence for the systematic and evolutionary studies of Impatiens species.

The Complete Chloroplast Genome and the Phylogenetic Analysis of Fimbristylis littoralis (Cyperaceae) Collected in Cherry Blossom Nursery.

Fimbristylis littoralis, also known as globe fringerush, is one of the most troublesome annual Cyperaceae weeds in dryland fields and nurseries in the Yangtze Plain, Middle and Lower in China. The chloroplast (cp) genome of F. littoralis, and even this genus, has not been studied yet. In this study, the feature of the cp genome of F. littoralis and its phylogenetic relationships has been reported for the first time. It exhibited a typical circular tetramerous structure, with 86 protein-encoding genes. There were 149 simple sequence repeats (SSRs) and 1932 long repeats (LRs) detected. The IR expansion and contraction revealed the uniqueness of F. littoralis because there is a special cross-boundary gene, rps3, located at the LSC/IRb junction. Phylogenetic and divergence time dating analysis showed the close relationship between F. littoralis and the genus Cyperus, as well as many evolutionary directions of Cyperaceae family plants. The most recommended chemical method for removing this weed from nurseries is to spray 13 g ai ha-1 (the amount of active ingredient applied per hectare) of saflufenacil before emergence or 7.5 g ai ha-1 of halosulfuron-methyl after emergence. In conclusion, this study was the first to report the complete cp genome of a plant in the genus Fimbristylis. Our findings also provided valuable biological information for studying the phylogenetic relationships and evolution among the family Cyperaceae.

Exploring the Complete Chloroplast Genomes of Key Lamiaceae Species Uncovers the Secrets of Evolutionary Dynamics and Phylogenetic Relationships

Abstract Chloroplast genome analysis provides crucial insights into plant evolution, classification, and conservation strategies. This study aimed to conduct a comprehensive comparative analysis of chloroplast genome architecture, gene content, and evolutionary relationships among five species of Lamiaceae (Lavandula angustifolia, Mentha × piperita, Ocimum × africanum, Salvia japonica, and Thymus serpyllum). Complete chloroplast genome sequences were retrieved from the NCBI database and analyzed using a systematic bioinformatics pipeline. Genome annotation was performed using Geneious Prime software, while repetitive sequence analysis was conducted using Tandem Repeats Finder. Phylogenetic relationships were reconstructed using MEGA software, implementing both the DualBrothers model and Neighbor-Joining method. The analyzed genomes exhibited the characteristic quadripartite structure, with sizes ranging from 152,048 to 153,995 base pairs and GC content between 37.8 and 38.0%. Each genome contained 131–134 genes, including 50 protein-coding sequences, 8 rRNA genes, and 37 tRNA genes. Comparative analysis revealed region-specific GC content variations, with IR regions showing the highest (43.0–43.4%), followed by LSC (35.9–36.2%) and SSC regions (31.6–32.1%). Codon usage analysis demonstrated a significant bias toward T/C-ending codons, particularly TTT, AAA, and AAT, correlating with the high AT content. Notable variations were observed at the LSC/IR/SSC junction regions, attributed to IR expansion and contraction. Molecular clock analyses indicated consistent evolutionary rates across the studied species. These findings provide valuable insights into the molecular evolution of Lamiaceae chloroplast genomes and establish a foundation for future research in plant molecular biology, systematic studies, and conservation efforts.

Comprehensive characterization and phylogenetic analysis of the complete plastomes of two ant–orchids, Caularthron bicornutum and Myrmecophila thomsoniana

BackgroundMyrmecophytes, characterized by specialized structures like hollow stems that facilitate mutualistic relationships with ants, serve as an important system for studying ant-plant interactions and the adaptation mechanisms. Caularthron and Myrmecophila are exemplary myrmecophytes within Orchidaceae. Previous studies suggested a genetic relationship between these two genera, placing them within Laeliinae (Epidendreae), yet the precise phylogenetic positioning remained uncertain. The absence of available plastome resources has hindered investigations into plastome evolution and phylogeny.ResultsIn this study, we sequenced and assembled the complete plastomes of Caularthron bicornutum and Myrmecophila thomsoniana to elucidate their plastome characteristics and phylogenetic relationships. The determined plastome sizes were 150,557 bp for C. bicornutum and 156,905 bp for M. thomsoniana, with GC contents of 37.3% and 37.1%, respectively. Notably, M. thomsoniana exhibited a distinctive IR expansion and SSC contraction, with the SSC region measuring only 4532 bp and containing five genes (ccsA, ndhD, rpl32, psaC, and trnL-UAG), a unique feature observed for the first time in Epidendreae. Comparative analyses with species from the related genus Epidendrum revealed that C. bicornutum plastome exhibited conserved genome size, GC content, gene content, and gene order. A total of 32 and 33 long sequence repeats, 50 and 40 tandem repeats, and 99 and 109 SSRs were identified in the plastomes of C. bicornutum and M. thomsoniana, respectively. The RSCU analysis demonstrated a consistent pattern in both plastomes, with 29 out of 30 codons with RSCU values greater than 1 featuring A/U at the third codon position. Leucine was the most prevalent amino acid, while Cysteine was the least common. Four potential DNA barcoding regions with Pi values exceeding 0.07, namely ycf1, ccsA–psaC, petN–psbM, and accD–psaI, were identified for subsequent phylogenetic reconstructions within Laeliinae. Phylogenetic analysis underscored the close relationships among Caularthron, Epidendrum, and Myrmecophila.ConclusionsThis study represents the first comprehensive analysis of the plastome characteristics of Caularthron bicornutum and Myrmecophila thomsoniana. Through our characterization and phylogenetic analyses, we unveiled the unique IR expansion/SSC contraction and further elucidated their phylogenetic positions. Our research contributes significant data and insights into the dynamic evolution of ant–orchid plastomes and the phylogeny of the Laeliinae.

Comparative and phylogenetic analyses of plastid genomes of the medicinally important genus Alisma (Alismataceae).

Alisma L. is a medicinally important genus of aquatic and wetland plants consisting of c. 10 recognized species. However, largely due to polyploidy and limited taxon and gene sampling, the phylogenomic relationships of Alisma remain challenging. In this study, we sequenced 34 accessions of Alismataceae, including eight of the ten species of Alisma, one species of Echinodorus and one species of Luronium, to perform comparative analyses of plastid genomes and phylogenetic analyses. Comparative analysis of plastid genomes revealed high sequence similarity among species within the genus. Our study analyzed structural changes and variations in the plastomes of Alisma, including IR expansion or contraction, and gene duplication or loss. Phylogenetic results suggest that Alisma is monophyletic, and constitutes four groups: (1) A. lanceolatum and A. canaliculatum; (2) the North American clade of A. subcordatum and A. triviale; (3) A. wahlenbergii and A. gramineum; and (4) A. plantago-aquatica from Eurasia and northern Africa with the eastern Asian A. orientale nested within it. Hence the results challenge the recognition of A. orientale as a distinct species and raise the possibility of treating it as a synonym of the widespread A. plantago-aquatica. The well-known Alismatis Rhizoma (Zexie) in Chinese medicine was likely derived from the morphologically variable Alisma plantago-aquatica throughout its long history of cultivation in Asia. The plastome phylogenetic results also support the tetraploid A. lanceolatum as the likely maternal parent of the hexaploid eastern Asian A. canaliculatum.

Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats.

The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of Eomecon chionantha, while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

BackgroudPaeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution.MethodsIn this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia.ResultsRanging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group.ConclusionsOverall, this study’s research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.

Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa

Chloroplast genomes for 3 Bidens plants endemic to China (Bidens bipinnata Linn., Bidens pilosa Linn., and Bidens alba var. radiata) have been sequenced, assembled and annotated in this study to distinguish their molecular characterization and phylogenetic relationships. The chloroplast genomes are in typical quadripartite structure with two inverted repeat regions separating a large single copy region and a small single copy region, and ranged from 151,599 to 154,478 bp in length. Similar number of SSRs and long repeats were found in Bidens, wherein mononucleotide repeats (A/T), forward and palindromic repeats were the most in abundance. Gene loss of clpP and psbD, IR expansion and contraction were detected in these Bidens plants. It seems that ndhE, ndhF, ndhG, and rpl32 from the Bidens plants were under positive selection while the majority of chloroplast genes were under purifying selection. Phylogenetic analysis revealed that 3 Bidens plants clustered together and further formed molophyletic clade with other Bidens species, indicating Bidens plants might be under radiation adaptive selection to the changing environment world-widely. Moreover, mutation hotspot analysis and in silico PCR analysis indicated that inter-genic regions of ndhD-ccsA, ndhI-ndhG, ndhF-rpl32, trnL_UAG-rpl32, ndhE-psaC, matK-rps16, rps2-atpI, cemA-petA, petN-psbM were candidate markers of molecular identification for Bidens plants. This study may provide useful information for genetic diversity analysis and molecular identification for Bidens species.

Complete chloroplast genome sequences of the medicinal plant Aconitum transsectum (Ranunculaceae): comparative analysis and phylogenetic relationships

BackgroundAconitum transsectum Diels. (Ranunculaceae) is an important medicinal plant that is widely used in traditional Chinese medicine, but its morphological traits make it difficult to recognize from other Aconitum species. No research has sequenced the chloroplast genome of A.transsectum, despite the fact that phylogenetic analysis based on chloroplast genome sequences provides essential evidence for plant classification.ResultsIn this study, the chloroplast (cp) genome of A. transsectum was sequenced, assembled, and annotated. A. transsectum cp genome is a 155,872 bp tetrameric structure including a large single copy (LSC, 87,671 bp) and a small single copy (SSC, 18,891 bp) section, as well as a pair of inverted repeat sequences (IRa and IRb, 25,894 bp each). 131 genes are encoded by the complete cp genome, comprising 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The most favored codon in the A. transsectum cp genome is AUG, and 46 repeats and 241 SSRs were also identified. The A. transsectum cp genome is similar in size, gene composition, and IR expansion and contraction to the cp genomes of seven Ranunculaceae species. Phylogenetic analysis of cp genomes of 28 plants from the Ranunculaceae family shows that A. transsectum is most closely related to A. vilmorinianum, A. episcopale, and A. forrestii of Subgen. Aconitum.ConclusionsOverall, this study provides complete cp genome resources for A. transsectum that will be beneficial for identifying potential.

Plastome evolution and phylogeny of the tribe Ruteae (Rutaceae).

Rutaceae is a large family, and the genus-level classification in the subfamilies or tribes of this family is not unified based on different taxonomic treatments. Until now, phylogenetic relationships of some genera in traditional tribe Ruteae have not been clearly resolved. In this study, seven new complete plastomes of this tribe were sequenced, and a comparative analysis was performed to investigate their plastome characteristics and evolution. In addition, we inferred the phylogenetic relationships of Ruteae based on complete plastome and nuclear ITS data. All plastomes exhibited a typical quadripartite structure and were relatively conserved in their structure and gene arrangement. Their genome sizes ranged from 154,656 bp to 160,677 bp, and the size variation was found to be associated with differences in IR expansion and gene loss. A total of 112 to 114 genes were identified in the genomes, including 78 to 79 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 2 pseudogenes. Sequence divergence analysis indicated that non-coding regions exhibited a higher percentage of variable characters, and nine non-coding and six coding regions were identified as divergent hotspots. Phylogenetic results based on different datasets showed that this tribe was divided into three reciprocally exclusive groups. The phylogenetic analyses between plastome and nuclear ITS data were partly incongruent with each other. This study provides new insights into plastome evolution of Ruteae as well as Rutaceae. The availability of these plastomes provides useful genomic resources for molecular DNA barcodes and phylogenetically informative markers and deepens our understanding of the phylogeny in Ruteae.

Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes.

The chloroplast (cp) is an autonomous plant organelle with an individual genome that encodes essential cellular functions. The genome architecture and gene content of the cp is highly conserved in angiosperms. The plastome of Corydalis belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of Corydalis chloroplast genomes. Therefore, the Corydalis platycarpa cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty Corydalis plastomes. Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the Corydalis species. By contrast, the plastomes of its closely related subfamily Papaveroideae and other Ranunculales taxa are highly conserved. On the other hand, the synapomorphy characteristics of both accD and the ndh gene loss events happened in the common ancestor of the Corydalis and sub-clade of the Corydalis lineage, respectively. The Corydalis-sub clade species (ndh lost) are distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The phylogenetic analysis and divergence time estimation were also employed for the Corydalis species. The divergence time of the ndh gene in the Corydalis sub-clade species (44.31 - 15.71 mya) coincides very well with the uplift of the Qinghai-Tibet Plateau in Oligocene and Miocene periods, and maybe during this period, it has probably triggered the radiation of the Corydalis species. To the best of the authors' knowledge, this is the first large-scale comparative study of Corydalis plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of Corydalis species.

Phylogenomics, plastome structure and species identification in Mahonia (Berberidaceae)

BackgroundElucidating the phylogenetic relationships within species-rich genera is essential but challenging, especially when lineages are assumed to have been going through radiation events. Mahonia Nutt. (Berberidaceae) is a genus with cosmopolitan distribution, comprising approximately 100 species, two of which are known as Caulis Mahoniae (M. bealei and M. fortunei) with crucial pharmacological significance in Chinese herbal medicine. Mahonia is a taxonomically challenging genus, and intrageneric phylogenetic relationships still need to be explored using genome data. Universal DNA barcodes and floral morphological attributes have limited discriminatory power in Mahonia.ResultsWe sequenced 17 representative plastomes and integrated three published plastome data together to conduct comparative and phylogenetic analyses. We found that Mahonia and Berberis share a large IR expansion (~ 12 kb), which is recognized as a typical character of Berberideae. Repeated sequences are revealed in the species of Mahonia, which are valuable for further population genetic studies. Using a comparative plastome analysis, we determined eight hypervariable regions whose discriminative power is comparable to that of the whole plastid genomes. The incongruence of the ITS and the plastome tree topologies may be ascribed to ancestral hybridization events and/or to incomplete lineage sorting. In addition, we suggest that leaf epidermal characters could help to distinguish closely related species in Mahonia.ConclusionsWe propose an integrative approach combining special barcodes and micromorphological traits to circumscribe Mahonia species. The results cast a new light on the development of an integrative method for accurate species circumscription and provide abundant genetic resources for further research on Mahonia.

Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields.

Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution.

Experimental and Theoretical Evidence for Relativistic Catalytic Activity in C-H Activation of N-Phenylbenzamide Using a Cationic Iridium Complex.

This study elucidates that relativistic effect plays a key role in catalytic C-H activation using a cationic Ir complex. Experiments show that the cationic Ir(I)-diphosphine catalyst can be used for the deuterium substitution of N-phenylbenzamide, whereas a cationic Rh(I)-diphosphine catalyst is scarcely effective. Density functional theory calculations, including the relativistic effect, demonstrate a large difference in the reaction energy diagrams for the C-H activation of N-phenylbenzamide between the cationic Ir and Rh catalysts. In particular, the relatively low reaction barrier and considerably stabilized product obtained for the Ir catalysts are rationalized by strong Ir-C and Ir-H interactions, which originate from the relativistic self-consistent d-orbital expansion of Ir.

Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships

Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species of the genus are widely used for a wide range of medicinal and industrial aspects. At present, most studies related to the gene resources of Litsea are restricted to morphological analyses or features of individual genomes, and currently available studies of select molecular markers are insufficient. In this study, we assembled and annotated the complete chloroplast genomes of nine species in Litsea, carried out a series of comparative analyses, and reconstructed phylogenetic relationships within the genus. The genome length ranged from 152,051 to 152,747 bp and a total of 128 genes were identified. High consistency patterns of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) were discovered across the genus. Variations in gene length and the presence of the pseudogene ycf1Ψ, resulting from IR contraction and expansion, are reported. The hyper-variable gene rpl16 was identified for its exceptionally high Ka/Ks and Pi values, implying that those frequent mutations occurred as a result of positive selection. Phylogenetic relationships were recovered for the genus based on analyses of full chloroplast genomes and protein-coding genes. Overall, both genome sequences and potential molecular markers provided in this study enrich the available genomic resources for species of Litsea. Valuable genomic resources and divergent analysis are also provided for further research of the evolutionary patterns, molecular markers, and deeper phylogenetic relationships of Litsea.

Continuous Infrared Popping: Effect on Key Physicochemical Attributes of Popcorn

The effect of continuous infrared (Co-IR) popping at different powers [600, 700 and, 800 W (W) Co-IR power] and a constant distance from the sample (5 cm) on the key physicochemical properties of popcorn (Zea mays L. var. Everta) [popping properties, energy consumption, morphology (SEM), sensory properties, and color] was investigated. According to the results of popping properties, optimum treatment for Co-IR popping of popcorn was 700 W Co-IR power. Colors were significantly changed (P < 0.05) during Co-IR popping. The L*, a*, b*, ΔE, hue, and chroma values of Co-IR popped popcorn (700 W Co-IR power) were 71.40, −2.73, 15.44, 33.13 ± 1.92, −1.40 ± 0.29, and 15.68 ± 1.07, respectively. The minimal energy usage was attained at 0.013 kWh at 800 W Co-IR power. In SEM analysis, with increasing the IR lamp power, the cavity size was increased (the cavities number per unit area decreased). The largest increase in the popcorn cavity size was determined at 800 W Co-IR power. The highest consumer acceptance of Co-IR popped corns was obtained at 700 W Co-IR power. This is the first study on the Co-IR expansion technology for popcorn popping, and the findings show that the IR expansion method is very efficient in the popcorn popping process.

Plastome characteristics and species identification of Chinese medicinal wintergreens (Gaultheria, Ericaceae)

Plastome characteristics and species identification of Chinese medicinal wintergreens (Gaultheria, Ericaceae)

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.